Spaghetti Squash Mac and Cheese
Posted Jan 10, 2019, Updated Nov 11, 2024
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This easy spaghetti squash mac and cheese recipe is low-carb and keto-friendly! It’s creamy, cheesy and delicious!
I created this Spaghetti Squash Mac and Cheese as a satisfying, low-carb, alternative everyone’s favorite classic pasta dish (mac and cheese)!
This spaghetti squash mac and cheese recipe is a healthy & delicious dinner, side dish or meal prep idea! It’s perfect to reheat for lunch with a salad or side of veggies.
This recipe is also keto-friendly which is great if you are craving mac and cheese but need to eat a low-carb diet.
Spaghetti Squash Mac & Cheese: Ingredients & Substitutions
- Spaghetti Squash. I do not recommend making substituions for the spaghetti squash in this recipe! The only thing that might vary in regards to the squash is the size. You could use one very large 4 lb. squash and only cut it into two halves instead of four.
- Olive Oil. Avocado oil is a good substitute.
- Salted Butter. unsalted butter or ghee are good substitutes.
- All-purpose flour. gluten-free all-purpose flour, tapioca flour and cornstarch are all great substitutes and make thsi recipe gluten-free.
- Cheddar Cheese. Use your favorite cheese, some suggestions include: We like extra sharp cheddar in our house, as well as gouda, gruyere, etc.
How to Make Spaghetti Squash Mac and Cheese
We’ll walk through how to make spaghetti squash mac and cheese step-by-step, and don’t forget to watch the video.
Bake the Spaghetti Squash
The first step in this recipe is to roast the spaghetti squash. Cut each squash into two equal halves lengthwise. Since the recipe will be baked inside of the shells, it’s important to try to keep them intact and in a good shape.
Next, use a firm metal spoon or even an ice cream scooper and scrape the insides out of the squash as you would before carving a pumpkin on Halloween.
Throw the insides/seeds away in the garbage. I don’t recommend putting them down the garbage disposal, as the seeds are pretty tough.
Spray or brush the inside of each half wiht olive oil then sprinkle the the squash with garlic powder, sea salt and pepper. (or any other spices you choose).
After coating the inside with oil & spices, flip the spaghetti squash halves over so they are face-down in a large baking sheet.
Pour boiling water into the pan to fill it so that about ½” of the bottom of the spaghetti squash is submerged in water. Baking the Spaghetti Squash in water helps make it moist and easy to shred.
Next, cover the baking sheet with foil (to retain the water as long as possible) and place in the preheated oven. Roast for 45-60 minutes (depending on the size of your squash).
You will know the spaghetti squash is cooked when you can easily press the top down with your hand and it stays depressed.
Shred the Spaghetti Squash
Next, very carefully take a fork and run it lengthwise across the spaghetti squash until all the insides are shredded (as pictured below).
Since the cheese sauce will be mixed with the squash inside of the shells and baked, it’s important to shred the squash very carefully and gently to avoid breaking the shells.
Make the Cheese
I recommend making the cheese sauce while the squash is roasting in the oven to save time, preferably in the last 10 minutes of baking.
To make the cheese sauce, start by making a roux. Melt the butter, mix the dry ingredients together and then add them to the butter in the saucepan.
Use a wire whisk and whisk until the dry ingredients are incorporated into the melted butter. Then cook for about 1 minute, or until bubbles begin to form in the mixture (see picture below on the right hand side).
Next, pour the milk into the roux in the saucepan, whisking constantly. Cook the milk/roux mixture for 3 to 5 minutes, until it becomes thick.
Once the milk mixture is thick, add the shredded cheese and turn off the heat (or at least reduce it to low). Whisk until the cheese is melted and the sauce is smooth.
The mixture (before the cheese is added) will release steam as it cooks. This is part of the thickening process (water evaporating) and is normal and critical to a thick melty cheese sauce!
The cheese sauce will also thicken as it cools, which is something to be aware of if you prepare it long before the spaghetti squash has finished roasting. If it becomes too thick as it sits, simply re-warm it on the burner over low heat.
Assemble Spaghetti Squash Mac & Cheese
Add ½ cup of the cheese sauce to each of the four spaghetti squash halves – distributing it evenly.
For the small spaghetti squashes I used (about 2 pounds each), I find ½ cup plus 2 Tablespoons sauce was the perfect amount to fill each squash-half and use all the sauce. However this amount will vary depending on the size of your squash.
Then, use a fork to gently incorporate the cheese sauce into the shredded spaghetti squash. As you can see, the mixture should be thick and not at all runny.
Next, place the cheesy spaghetti squash halves on a large baking sheet.
Sprinkle some more cheese on top of each squash and then bake in the preheated oven until the cheese is melted.
The longer you bake the Spaghetti Squash Mac and Cheese recipe, the firmer the cheese on top will be. Use your discretion and bake as long as it takes to reach the texture you would enjoy the most.
Serve
Serve plain or with a garnish of fresh herbs or parmesan cheese alongside your favorite dinner recipes, salads, etc. Here are some suggestions:
- On the side of this balsamic pot roast (a family favorite)!
- Serve it with a salad like this kale salad or brussel sprouts salad.
- For a truly kid-friendly dinner, serve it with these healthy Sloppy Joes!
- Add some balsamic roasted veggetables!
- This oven-roasted broccoli pairs perfectly with this spaghetti squash mac and cheese!
- Balsamic roasted brussels sprouts taste amazing with this dish!
Store/Freeze
Store in an airtight container in the refrigerator for 3-5 days, or in the freezer for up to 1 month.
Reheat in a covered baking dish in the oven set to 300 degrees Fahrenheit until warmed through.
Spaghetti Squash Mac & Cheese FAQs
Spaghetti squash is very low carb. ½ cup of spaghetti squash contains roughly 20 calories and 5 g of carbs. So while it fits in the keto diet, you still need to watch your portion size.
½ cup baked spaghetti squash has 20 calories and 5 g of carbs.
I am a proponent of everything in moderation. I would not say that pasta is “bad for you!” However, spaghetti squash definitely has a few health benefits:
It’s lower in calories (only 40 calories in 1 cup as opposed to over 200 in most cases for pasta)
Relatively high in fiber (1 cup has 2.2 g of fiber).
Contains many vitamins & minerals (vitamin C, potassium, iron, Vitamin B6, manganese, etc.)
Very low in carbs (only 5 g in ½ cup).
Disclaimer: I am not an expert on the Keto diet, but from what I understand the main concern is consuming less than 30 g of carbs per day.
The recipe calls for whole milk and there is 11 g of carbs per serving (without making a low-carb substitute for the flour). You can use heavy cream instead of whole milk, which has an even lower carb count and tapioca flour instead of all-purpose flour…and get a net carb count of 9.4 g per serving.
You can also try substituting unsweetened coconut milk, almond milk, pea milk, hemp milk or flax milk.
You will know the spaghetti squash is cooked when you can easily press the top down with your hand and it stays depressed.
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Spaghetti Squash Mac and Cheese
Ingredients
Spaghetti Squash
- 2 spaghetti squash (about 2 pounds each)
- 1 Tablespoon olive oil
- ½ teaspoon fine sea salt (or to taste)
- ½ teaspoon garlic powder
- ¼ teaspoon pepper (or to taste)
Cheese Sauce
- 2 Tablespoons salted butter
- 2 Tablespoons all-purpose flour (or gluten-free all-purpose flour, tapioca flour or cornstarch)
- ½ teaspoon fine sea salt
- ¼ teaspoon garlic powder
- 1 ½ cups whole milk
- 2 ½ cups sharp cheddar cheese divided
Instructions
Roast the Spaghetti Squash
- Preheat oven to 400 degrees F.
- Cut both spaghetti squash in half and remove the seeds (scoop them out with a metal spoon).
- Brush the inside with olive oil (or spray with an olive oil spray) and sprinkle with sea salt and pepper.
- Place cut-side down in a baking dish.
- Fill baking dish ¼” with water.
- Cover baking dish with aluminum foil.
- Bake in the preheated oven for 45-60 minutes or until the squash is soft to the touch (it will compress down when pushed lightly).
- Remove from the oven and turn the cut-side to the top.
- Let cool.
- Use a fork to shred the spaghetti squash, being careful not to poke holes in the shell.
- Leave shredded spaghetti squash in the shell while you make the cheese sauce.
Make the Cheese Sauce
- Preheat oven to 375 degrees F.
- In a small bowl, combine flour sea salt and garlic powder. Set aside.
- Melt butter in a medium saucepan over medium heat.
- Add dry ingredients and whisk to combine.
- Whisk constantly until ingredients just start to brown (about 1-2 minutes).
- Add milk and whisk until mixture is smooth.
- Continue cooking over medium-high heat until the mixture comes to a boil and starts to thicken (about 3-5 minutes).
- Once mixture is thick, add 2 cups of shredded cheese and whisk until the cheese is completely melted.
- Once cheese sauce is smooth, remove the saucepan from the heat.
Assemble
- Distribute cheese sauce evenly among the four halves of shredded spaghetti squash (with the size squashes I had, I used about ½ cup plus 2 TBS of cheese sauce for each of the four halves).
- Use a fork to gently stir the cheese sauce into each half of shredded spaghetti squash.
- Once the sauce is evenly distributed in the squash, use the fork or a spatula to smooth out the surface of each squash half.
- Top with remaining ½ cup of cheese.
Bake & Serve
- Bake in the preheated oven for 15 minutes, or until the cheese on the top is melted and lightly brown.
- Serve warm.
Video
Notes
- Spaghetti Squash. I do not recommend making substituions for the spaghetti squash in this recipe! The only thing that might vary in regards to the squash is the size. You could use one very large 4 lb. squash and only cut it into two halves instead of four.
- Olive Oil. Avocado oil is a good substitute.
- Salted Butter. unsalted butter or ghee are good substitutes.
- All-purpose flour. gluten-free all-purpose flour, tapioca flour and cornstarch are all great substitutes and make thsi recipe gluten-free.
- Cheddar Cheese. Use your favorite cheese, some suggestions include: sharp cheddar, gouda, gruyere, etc.
Nutrition
Nutrition information is automatically calculated, so should only be used as an approximation.
Tried this dish today and it was AMAZING! We are pretty strict about carbs though, so instead of using any flour we created a keto “roux” by mixing cream cheese, butter, and heavy cream together with the cheese. It came out sooooo good. Definitely will be making this again soon.
being lactose free my self , will almond milk just as well. making this tonight. thank you
Excellent five star recipe!! I mixed 1/2 tbsp. of greek yogurt with 2% milk in stead of whole milk. I used whole wheat flour, which did give the cheese sauce a different look, but we don’t mind that since it’s healthier and tastes great ! I used 1/4 less cheese in the cheese sauce than was called for and I omitted to place it back in the oven since I didn’t have enough cheese. The end result was fantastic nonetheless! I also forgot to cover the squash in the oven with aluminum. The shell was hard enough to not get pierced at all. I will definitely be making this again, thanks for sharing!
Can I use 2% milk instead of whole milk?
Yes!
My goodness, what a delicious way to eat our Spaghetti Squash Fromm the garden!! I didn’t have enough cheddar cheese so I just used what I had, a little sharp cheddar, Mexican blend cheese and some quesadilla melting cheese!! We will make it again!
Thank you so much! Now I wish we grew spaghetti squash in our garden! Next year! 😉
I’ve made this recipe for my family twice now and as delicious as it was the first time, the second time it was even better. The first time I completely missed the part about baking the spaghetti squash for an additional 15 minutes with the roux. We really found that the additional baking time and adding more cheese on top brought this dish to the next level. I can’t wait to make again. Thanks for sharing such a fun delicious recipe.
Can you make this in a baking dish instead of the squash halves? what would need to adjust?? thanks!
Yes of course!
This recipe is absolutely delicious! I love spaghetti squash and have made it in several ways, but this is the best! It’s so creamy and delicious, and makes a great side dish for chicken or steak! Will definitely keep this recipe and make again! I wouldn’t change a thing!
Can I use Almond flour instead?
Technically yes you can give it a whirl. I’d recommend and all-purpose gluten-free flour or tapioca/cornstarch instead though!
I have to say that this might help my family like spaghetti squash. It’s SOOO cheesy. 🙂 I LOVE cheesy pasta so much.